3DNA was created in the hope that it
will be useful, but without any guarantees. Nothing is perfect, and we
strive to improve its functionalities. Any comments, constructive
suggestions, and bug reports are welcome.

cf_7methods.par: parameters of
the seven most frequently used nucleic acid analysis
programs-CEHS, CompDNA, Curves, FreeHelix, NGEOM, NUPARM, RNA-calculated based on the standard reference
frame. Note that the numerical values are very similar

ref_frames.dat: position and
orientation of each base-pair reference frame, useful for re-orienting
the structure with frame_mol

poc_haxis.r3d: global linear
helical axis with average radii of P, O4' and C1' atoms for input to
Raster3D.

hstacking.pdb: multiple
structures in PDB format composed of each dinucleotide step with
reference to its middle helical frame

stacking.pdb: multiple structures
in PDB format composed of each dinucleotide step with reference to its
middle step frame. Used for generating "standardized" stacking
diagrams

A complete helical turn of DNA having Twist = 36°, showing the
effects of introducing uniform Roll and Slide at each step. [Calladine
& Drew (1997), "Understanding DNA: The Molecule and How It Works",
2nd Edition, pp56.]

Two complete helical turns of DNA, with a curvature of 45° per
turn, or 4.5° per step on average. Such tight curvature may be
achieved, in principle, by any of the distributions of Roll angle shown
in parts (a) to (d). [Calladine & Drew (1997), "Understanding DNA:
The Molecule and How It Works", 2nd Edition, pp78.]

Fiber models: 55 fiber models can be
conveniently generated with the program fiber.

Stacking diagrams: based on the file stacking.pdb generated with analyzeshown above, the
following image can be produced directly with
stack2img and rendered with Raster3D.

Base multiplets can be automatically identified and oriented in the
best view with the utility program find_pair. The following image was generated with
r3d_atom and rendered with Raster3D.

Double helical regions are automatically identified by find_pair, and relatively straight helices can be
rendered as cylinders, as shown in the following example of a nucleic acid
junction (Nowakowski et al. (2000) J Mol Biol.,
300(1), pp.:93-102).

The schematic output from 3DNA progams, such as stack2img,
r3d_atom and blocview, can also be fed directly to
PyMol to get high-quality
ray-traced images, as shown in the following examples: